Number years ago, would use Apply Refund to a future year tax return with good results. Then I READ a VERY GOOD - NO EXCELLENT ARTICLE, that explained WHY NOT A GREAT IDEA. For the very reason you're starting to experience on the 1040X Amended Return! If the tax return and refund gets delayed then it impacts future years, risking penalties and interest. Moreover, if a prior year's return is audited with changes then a snowball event rolls backwards to other prior years, as well possibly forward to future years. Not worth the headache.

Also since Covid-19 seen IRS Identification and/or Amendment Units stall for 2 to 3 years whereby the tax return sits on their desk not processing, even when there's been contact. Again, don't use Apply Refund.